Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001243
UniProt IDP84243
Primary gene name(s)H3F3A; H3F3B
Synonym gene name(s)H3.3A, H3F3;, H3.3B
Protein nameHistone H3.3
Protein functionVariant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. {ECO:0000269|PubMed:14718166, ECO:0000269|PubMed:15776021, ECO:0000269|PubMed:16258499}.
Subcellular locationNucleus. Chromosome.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P84243
Gene Ontology
(Biological Process)
Complete annatation
blood coagulation [GO:0007596];
cellular protein metabolic process [GO:0044267];
chromatin silencing at rDNA [GO:0000183];
DNA replication-independent nucleosome assembly [GO:0006336];
gene silencing by RNA [GO:0031047];
negative regulation of gene expression, epigenetic [GO:0045814];
nucleosome assembly [GO:0006334];
positive regulation of cell growth [GO:0030307];
positive regulation of gene expression, epigenetic [GO:0045815];
telomere organization [GO:0032200]
Gene Ontology
(Molecular Function)
Complete annatation
histone binding [GO:0042393];
nucleosomal DNA binding [GO:0031492];
RNA polymerase II core promoter sequence-specific DNA binding [GO:0000979];
RNA polymerase II distal enhancer sequence-specific DNA binding [GO:0000980]
Gene Ontology
(Cellular Component)
Complete annatation
extracellular exosome [GO:0070062];
extracellular region [GO:0005576];
nuclear chromosome [GO:0000228];
nuclear chromosome, telomeric region [GO:0000784];
nuclear nucleosome [GO:0000788];
nucleoplasm [GO:0005654];
nucleosome [GO:0000786];
nucleus [GO:0005634];
protein complex [GO:0043234]
Protein-protein interaction109272;109273
Phylogenetic treeP84243
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
      unknown
Brass et al., Science, 2008
      unknown
Smith et al., J. Immunol, 2010
      unknown
Interferon-stimulated
gene status
Lu et al., J. Virol., 2011
      Folds changes 8h: unknown; Folds changes 16h: unknown; Tested: unknown;
Schoggins JW and Rice CM, Curr. Opin. Virol., 2011
      Targeted viruses: unknown
      Viral life cycle: unknown
      Mechanism related to antiviral activity: unknown
Anti-viral restriction factor Liu et al., Retrovirology, 2011
      unknown (Triplicates)

Gene Expression Profile       top

            Up-regulated;            Down-regulated

For brief introduction to each study, please go to the help page.

Gene expression during HIV latency

(1). Mohammadi et al., PLoS Pathog., 2014

Differentially expressed transcripts (Pairwise) during latency and subsequent viral reactivation using several agents - Primary CD4+ T-cell based model


DMSO: Dimethyl suloxyde (negative control) - 0.0033% final
SAHA: Vorinostat (Histone deacetylase inhibitor) - 0.5 μM
CD3: TCR Stimulation by IL-2+ antiCD3/anti-CD28 antibodies
IL7: Interleukin-7 based stimulation
DISU: Disulfiram (alcohol dehydrogenase inhibitor) - 0.5 μM
AZA: 5-azacytidine (AZA; DNA methylation inhibitor) - 1 μM
Experimental Condition Log2 Fold Change P value Adjusted P value
AZA vs. CD30.83500053490620.01115828017114660.0286113641952232
AZA vs. DISU-0.04895319154580950.8465114559947040.987834633347355
AZA vs. IL70.06605306609027420.7301416671732660.999311006273513
AZA vs. SAHA0.4731712411483260.05299174574473630.280034793870391
DISU vs. CD3-0.8977960004509440.01384678792943350.0381131276777585
DISU vs. IL70.1065730056107790.6722038134188440.909974181689034
DISU vs. SAHA0.5232649172305670.07259917296460580.340655198865557
DMSO vs. AZA-0.02578295964120930.8770729194004421
DMSO vs. CD3-0.8751313277131630.006500798924398480.0171664392280566
DMSO vs. DISU0.02061242166142490.93266518066150.991044421109467
DMSO vs. IL70.09946491134363740.5786116278900550.905672503991634
DMSO vs. SAHA0.4924363378772620.03725876408545840.211338665235959
HIV vs. Mock in Activation-0.0634345024671410.9186701180722940.999983755607037
HIV vs. Mock in Latency-0.2739843912740490.09547279653234250.999834320637052
IL7 vs. CD3-0.7602318617699520.0183965341486120.0489394562693308
SAHA vs. CD3-0.3875486800959850.2729279731402710.385228969821286
SAHA vs. IL70.4023837356575010.09916751946149620.285781346917135
(2). Iglesias-Ussel et al., J. Virol., 2013

Up and Downregulated transcripts during Latency (Latently infected CD4+ T cells vs Uninfected)- Primary CD4+Tcell based model
Log2 Fold Change P Value
unknown unknown

Gene expression during HIV infection and replication

(1). Imbeault et al., PloS Pathog., 2012

Transcriptomic profiling of HIV-1 infected CD4+ T cells - Primary CD4+ T cells
Experiment type Log2 Fold Change P Value Adjusted P Value
Infected vs. Mock unknown unknown unknown
Infected vs. Bystander -0.771 1.05E-05 1.19E-04
(2). Lefebvre et al., J. Virol., 2011

Transcriptome analysis of T-cell line (Sup T1)
Log2 Fold Change unknown
(3). Li et al., J. Immunol., 2013

Lymphatic tissue
Acute Fold Change Acute P Value Asymt Fold Change Asypt P Value AIDS Fold Change AIDS P Value
unknown unknown unknown unknown unknown unknown
(4). Chang et al., MBio., 2011

Transcriptome analysis of T-cell line (Sup T1)

Derived from Sherrill-Mix et al., BMC Retrovirol., 2015 cross validation
Up-regulated (True) FALSE
(5). Sherrill-Mix et al., BMC Retrovirol., 2015

Deep RNA-seq analysis of primary human T cell infected with low passage HIV isolate HIV89.6 - Primary CD4+ T cell based
Test Status Log2 Fold Change P Value
OK 0.235719 0.0911491
(6). Rotger et al., PLoS Pathog., 2010

Genome-wide mRNA expression of CD4+ T cells from HIV-infected patient
(Genes differentially expressed (at adjusted p<0.01) according to the empirical Bayes approach)
Log2 Fold Change P Value
unknown unknown

Proteomic/Transcriptomics studies indicating differentially expressed genes mediated by HIV

(1). Greenwood et al., Elife, 2016

Activated (CD3/CD28) Primary human CD4+ T cells infected with pNL4-3-dE-EGFP. The table shows the complete (unfiltered) TMT (tandem mass tag)-based proteomic time course dataset
6 h 24 h 48 h 72 h RTi
1.105 1.175 1.08 1.238 1.175
(2). Navare et al., Virology, 2012

SUP-T1 cell line
FC-4hpi P-value FC-8hpi P-value FC-20hpi P-value Category
unknown unknown unknown unknown unknown unknown unknown
(3). Hyrcza et al., J. Virolo., 2007

Primary human CD4+ and CD8+ T Cells
Affymetrix Prob ID Fold Change In CD8? Category
unknown unknown unknown unknown

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

not found

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
2L43 NMR - A=2-13.
3ASK X-ray 2.9Å P/Q/R=2-14.
3ASL X-ray 1.4Å B=2-12.
3AV2 X-ray 2.8Å A/E=1-136.
3JVK X-ray 1.8Å C=13-20.
3MUK X-ray 1.7Å D=22-29.
3MUL X-ray 1.6Å D=13-20.
3QL9 X-ray 0.9Å C=2-16.
3QLA X-ray 1.6Å C/F=2-16.
3QLC X-ray 2.5Å C/D=2-16.
3WTP X-ray 2.6Å E=1-136.
4GNE X-ray 1.4Å B=2-8.
4GNF X-ray 1.5Å C=2-16.
4GNG X-ray 1.7Å B/F=2-16.
4GU0 X-ray 3.1Å E/F=2-27.
4GUR X-ray 2.5Å C=2-22.
4GUS X-ray 2.2Å C=2-22.
4GY5 X-ray 2.9Å E/F=2-18.
4H9N X-ray 1.9Å A=2-136.
4H9O X-ray 2.0Å A=2-136.
4H9P X-ray 2.2Å A=2-136.
4H9Q X-ray 1.9Å A=2-136.
4H9R X-ray 2.2Å A=2-136.
4H9S X-ray 2.6Å A/B=2-136.
4HGA X-ray 2.8Å B=1-136.
4L58 X-ray 1.4Å B=2-13.
4N4I X-ray 2.0Å B=20-43.
4O62 X-ray 1.7Å D=2-12.
4QQ4 X-ray 1.7Å C/D=2-16.
4TMP X-ray 2.3Å B/D=2-12.
4U7T X-ray 2.9Å F/G=2-13.
4W5A X-ray 2.6Å C/D/F=2-16.
5AY8 X-ray 2.8Å A/E=1-134.
5B32 X-ray 2.3Å A/E=1-136.
5B33 X-ray 2.9Å A/E=1-136.
5BNV X-ray 2.7Å A/D=58-136.
5BNX X-ray 2.3Å A=58-136.
5DWQ X-ray 2.3Å F/G=14-31.
5DX0 X-ray 2.0Å F/G/H/I=14-31.
5JA4 X-ray 2.4Å A=58-136.
5KDM X-ray 3.5Å A=2-136.

HIV-1 Interaction       (annotations from NCBI HIV-1 Interaction Database)      top

not found

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa05034 Alcoholism - Homo sapiens (human)
hsa05202 Transcriptional misregulation in cancer - Homo sapiens (human)
hsa05322 Systemic lupus erythematosus - Homo sapiens (human)
hsa05034 Alcoholism - Homo sapiens (human)
hsa05202 Transcriptional misregulation in cancer - Homo sapiens (human)
hsa05322 Systemic lupus erythematosus - Homo sapiens (human)
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